Campaign 2014 (PhD Chapter 1)


This series of files compile all analyses done during Chapter 1 for the local campaign of 2014:

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

2014 2016 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2016 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Abundances of Bipalponephtys neotena (Bneo) and Spisula solidissima (Ssol) were also considered (see IndVal and SIMPER results).

Statistics for each variable considered:

  Mean SD SE Median Min Max 95% CI
om 1.368 1.465 0.232 0.868 0.187 8.260 0.454
gravel 0.017 0.076 0.012 0.000 0.000 0.481 0.024
sand 0.148 0.358 0.057 0.000 0.000 1.000 0.111
silt 0.004 0.006 0.001 0.001 0.000 0.022 0.002
clay 0.830 0.361 0.057 0.992 0.000 1.000 0.112
arsenic 2.720 1.259 0.199 2.250 1.100 6.000 0.390
cadmium 0.116 0.045 0.007 0.110 0.030 0.220 0.014
chromium 65.520 29.623 4.684 63.200 10.900 143.300 9.180
copper 11.045 8.675 1.372 7.300 2.200 32.400 2.688
iron 64222.926 31677.444 5008.644 60284.230 14089.920 188857.220 9816.761
manganese 1412.044 1050.987 166.176 1106.625 251.670 5962.190 325.698
mercury 0.014 0.043 0.007 0.000 0.000 0.250 0.013
lead 4.308 2.945 0.466 3.110 1.020 12.180 0.913
zinc 53.163 23.870 3.774 45.150 15.900 101.500 7.397
S 20.475 7.906 1.250 18.500 6.000 35.000 2.450
N 640.975 703.306 111.202 176.500 14.000 2103.000 217.953
H 1.840 0.410 0.065 1.917 0.911 2.737 0.127
J 0.636 0.155 0.025 0.622 0.315 0.938 0.048

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Organic matter

Grain-size

Heavy metals

Species abundances

Diversity indices

2.2. Phylum frequencies

Conditions

Phylum abundances by condition
Phylum HI R
Annelida 20360 1135
Phoronida 1138 2
Arthropoda 883 749
Mollusca 361 743
Cnidaria 42 40
Bryozoa 8 22
Platyhelminthes 5 0
Echinodermata 4 139
Hemichordata 2 0
Chaetognatha 0 1
Nematoda 0 0
Nemertea 0 5
Sipuncula 0 0

Sites

Phylum abundances by site
Phylum P1 P2 P3 P4 R1 R2 R3 R4
Annelida 6065 7459 6155 681 43 106 926 60
Phoronida 408 317 412 1 0 0 1 1
Arthropoda 289 317 219 58 40 281 399 29
Mollusca 60 113 80 108 30 381 110 222
Cnidaria 13 11 9 9 11 15 7 7
Bryozoa 4 1 0 3 0 14 2 6
Echinodermata 4 0 0 0 20 65 49 5
Platyhelminthes 1 0 4 0 0 0 0 0
Chaetognatha 0 0 0 0 0 1 0 0
Hemichordata 0 0 2 0 0 0 0 0
Nematoda 0 0 0 0 0 0 0 0
Nemertea 0 0 0 0 0 5 0 0
Sipuncula 0 0 0 0 0 0 0 0

2.3. Species estimation curves

2.4. Principal Component Analysis

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

2.5. Non-metric Multidimensional Scaling

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species were deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  3  1  3  3  3  3  3  2  3  3  3  2  2  3  2  3  2  3  3  3  3  3

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  1  1  3  3  3  3  3  2  3  3  3  2  2  3  2  3  2  3  3  3  3  3

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 
##  1  2  1  1  1  1  2  1  1  1  2  3  2  2  2  3  3  2  2  2  2  2  2  3  2  3  3  3  3  3  3  3  3  3  3  2  2  3  3  3

Species

Stations with no species were deleted from this analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  1  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2


Elliot Dreujou

2020-01-20